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The Crystal structure of F46Y mutant of apo agroavidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 18% pentaerythritol ethoxylate,
0.05 M Bis Tris pH 5.9-6.0,
0.05 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.02 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.322 α = 90 b = 84.781 β = 90 c = 67.915 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 16M optical hatch 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID09 1.0723 ESRF ID09
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.66 44.76 98.6 0.99 15.5 4.3 53732
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.72 0.778 0.794
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3ew1 1.66 44.76 53763 2735 98.2 0.18033 0.17851 0.19 0.21467 0.2209 RANDOM 24.271
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.01 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.206 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_1_deg 6.933 r_long_range_B_refined 6.22 r_long_range_B_other 6.181 r_scangle_other 4.713 r_mcangle_it 3.566 r_mcangle_other 3.565 r_scbond_it 3.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.206 r_dihedral_angle_4_deg 19.168 r_dihedral_angle_3_deg 13.793 r_dihedral_angle_1_deg 6.933 r_long_range_B_refined 6.22 r_long_range_B_other 6.181 r_scangle_other 4.713 r_mcangle_it 3.566 r_mcangle_other 3.565 r_scbond_it 3.065 r_scbond_other 3.065 r_mcbond_it 2.45 r_mcbond_other 2.45 r_angle_refined_deg 1.693 r_angle_other_deg 1.539 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3771 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing